This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Oncomine™ Tumor Mutation Load Assay is a targeted NGS assay that provides an assessment of tumor mutation load and mutation signatures in a simple workflow. The assay contains coverage of 1.65mb across 409 genes.
The Oncomine™ Tumor Mutation Load Assay is a targeted NGS assay that provides an assessment of tumor mutation load and mutation signatures in a simple workflow. The assay contains coverage of 1.65mb across 409 genes.
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Oncomine™ Myeloid Research Assay is a comprehensive, targeted NGS assay designed to interrogates relevant DNA mutations and fusion transcripts associated with myeloid disorders in a quick and easy NGS run.
The Oncomine™ Myeloid Research Assay is a comprehensive, targeted NGS assay designed to interrogates relevant DNA mutations and fusion transcripts associated with myeloid disorders in a quick and easy NGS run. Our panel is comprised of 40 key DNA target genes and 29 driver genes in a broad fusion panel to cover all the major myeloid disorders: acute myeloid leukemia (AML), myeloid dysplastic syndrome (MDS), myeloproliferative neoplasms (MPN), chronic myeloid leukemia (CML), chronic myelomonocytic leukemia (CMML), and juvenile myelomonocytic leukemia (JMML).
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Oncomine™ Focus Assay is a targeted, multi-biomarker assay that enables detection of target hotspots, SNVs, indels, CNVs, and gene fusions across 52 genes relevant to solid tumors from DNA and RNA in a single workflow.
The Oncomine™ Focus Assay is a targeted, multi-biomarker assay that enables detection of target hotspots, SNVs, indels, CNVs, and gene fusions across 52 genes relevant to solid tumors from DNA and RNA in a single workflow. The content driven by the Oncomine™ Knowledgebase, which includes content aligned to approved therapies and indications.
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Oncomine™ Comprehensive Assay v3 is a targeted, multi-biomarker assay that enables the detection of relevant SNVs, indels, CNVs, gene fusions, and indels from 161 unique genes to help inform drug discovery research and clinical trial research programs.
The Oncomine™ Comprehensive Assay v3 is a targeted, multi-biomarker assay that enables the detection of relevant SNVs, indels, CNVs, gene fusions, and indels from 161 unique genes to help inform drug discovery research and clinical trial research programs. The assay includes kinase domain coverage to span the entire kinase domain in several critical receptor tyrosine kinases and representation of genes involved in DNA repair.
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Oncomine™ BRCA Research Assay uniquely empowers laboratories to detect all classes of mutations ( SNVs, InDels, and large exon/gene deletions/duplications) in one NGS workflow, removing the need to employ multiple technologies.
The Oncomine™ BRCA Research Assay uniquely empowers laboratories to detect all classes of mutations ( SNVs, InDels, and large exon/gene deletions/duplications) in one NGS workflow, removing the need to employ multiple technologies. The assay is designed to provide sensitive and comprehensive sample amplification of all coding regions of the human BRCA1 and BRCA2 genes.
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Oncomine TCR Beta-LR Assay is designed to measure T cell diversity and clonal expansion by sequencing T cell receptor beta chain rearrangements.
The Oncomine TCR Beta-LR Assay is designed to measure T cell diversity and clonal expansion by sequencing T cell receptor beta chain rearrangements. The assay is designed to efficiently capture all three complementarity determining regions of the TCR beta chain (CDR1, CDR2, CDR3) with high accuracy.
Note: The amplicon count and number of pools are dummy values.
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Oncomine™ Immune Response Research Assay is a targeted gene expression assay that enables immuno-oncology research through the quantitative evaluation of the expression of markers associated with different leukocyte subsets, antigen presentation, checkpoint pathways, and tumor progression.
The Oncomine™ Immune Response Research Assay is a targeted gene expression assay that enables immuno-oncology research through the quantitative evaluation of the expression of markers associated with different leukocyte subsets, antigen presentation, checkpoint pathways, and tumor progression. The assay measures the expression of genes involved in tumor-immune interactions, including the low-expressing genes involved in inflammatory signaling.
Note: The amplicon count and number of pools are dummy values.
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Oncomine™ TCR Beta SR – Assay is a robust, targeted next-generation sequencing (NGS) assay designed to accurately identify and measure the clonal expansion of tumor infiltrating lymphocytes (TILs) in formalin-fixed, paraffin-embedded (FFPE) samples.
The Oncomine™ TCR Beta SR – Assay is a robust, targeted next-generation sequencing (NGS) assay designed to accurately identify and measure the clonal expansion of tumor infiltrating lymphocytes (TILs) in formalin-fixed, paraffin-embedded (FFPE) samples. This assay identifies unique T cell clones through targeting the diverse complementary determining region 3 (CDR3) of the T cell receptor (TCR) gene locus in genomic DNA or RNA. The nucleotide sequence of the CDR3 region is unique to each T cell clone and codes for the part of the TCR beta chain that is involved in antigen recognition
Note: The amplicon count and number of pool are dummy values.
Ion AmpliSeq™ Microsatellite Instability Research Panel
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
Microsatellite instability (MSI) is associated with hypermutability of short DNA sequence repeats and defects related to the mismatch repair (MMR) system. This has been observed in diverse cancer types. The panel contains a single primer pool that amplifies a total of 76 amplicons to assess the MSI status from FFPE DNA of human cancer tissue sections.
Microsatellite instability (MSI) is associated with hypermutability of short DNA sequence repeats and is related to defects in the mismatch repair (MMR) system. MSI has been observed in diverse cancer types – including, but not limited to colorectal, gastric and endometrial cancers. Research studies have shown MSI-High to be predictive of response to immunotherapy. The Ion AmpliSeq™ Microsatellite Instability Research Panel contains a single primer pool that amplifies a total of 76 amplicons to assess the MSI status from DNA from formalin-fixed paraffin embedded (FFPE) human cancer tissue sections. This panel is compatible with Ion AmpliSeq™ Kit 2.0 and Ion AmpliSeq™ Kit Plus User Guide Protocols. To analyze the sequencing output from this panel, a Torrent Suite plugin under the name “MSICall” is available on the Themo Fisher Scientific Plugin store.See panel README for more information. For Research Use Only. Not for use in diagnostic procedures.
Design Date
October 2018
Publication:Poster presented at the 68th Annual Meeting of The American Society of Human Genetics, October 17, 2018 in San Diego, California: Evaluation of Microsatellite Instability (MSI) using Ion Torrent Sequencing technology
Author: Sameh El-Difrawy
Affiliation: Thermo Fisher Scientific
Recommended Configuration
BC: IonXpress; IonCode
Samples per Chip:
160 per Ion 540 chip
40 per Ion 530 chip
10 per Ion 520 chip
Sample Type
gDNA or FFPE DNA
Number of sample in publication
NA
Observed Performance
Panel uniformity: not critical for panel performance
Reads on-targets: not critical for panel performance
Input DNA required
10ng per sample.
One reference normal DNA library per sequencing run – we recommend NA12878, NA24385 or CEPH Individual 1347-02 (Catalog Number 403062) .
Disease Research Area: Cancer Research
Ion AmpliSeq™ Methylation Panel for Cancer Research
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
This panel analyses clinically relevant targets for identification of specific methylation patterns within a DNA sample. The panel contains 40 amplicons (including 2 control amplicons) to detect methylation status of 38 targets including targets associated with colon cancer, prostate cancer, Leukemia, and lymphoma.
Ion AmpliSeq™ Methylation Panel for Cancer Research analyzes clinically relevant targets using the bisulfite method for identifying specific methylation patterns within a DNA or FFPE DNA sample. With low DNA input, the panel provides high accuracy, ease of use, and short time to answer. This Ion AmpliSeq™ Methylation Panel protocol combines a one day bisulfite kit protocol with the one day Ion AmpliSeq™ Library Kit Plus protocol to create (NGS) libraries for target DNA methylation assessment during sequencing. Consult the bisulfite methylation library construction protocol using the Ion AmpliSeq™ Library Kit Plus and the protocol using the Ion AmpliSeq™ Kit for Chef DL8 for detailed instructions. The panel contains one pool containing 40 amplicons (including 2 control amplicons) to detect methylation status of 38 targets including targets associated with colon cancer, prostate cancer, leukemia, and lymphoma as published in Bock et al. 2016. The DNA methylation targets, evaluated in this technology benchmarking study by the BLUEPRINT Consortium, are highly validated to be reproducible and reliable cancer biomarkers by multiple assays, and therefore this panel serves as a targeted DNA methylation cancer panel and a reliable technical as well as biological reference. To analyze the sequencing output from this panel, a Torrent Suite plugin under the name “methylation_analysis” is available on the Themo Fisher Scientific Plugin store. For research use only. Not for use in diagnostic procedures.
Design Date
March 2019
Publication: Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nature Biotechnology 34, 726–737 (2016)
Author: Bock C, Halbritter F, Carmona FJ, Tierling S, Datlinger P, Assenov Y, Berdasco M, Bergmann AK, Booher K, Busato F, Campan M, Dahl C, Dahmcke CM, Diep D, Fernández AF, Gerhauser C, Haake A, Heilmann K, Holcomb T, Hussmann D, Ito M, Kläver R, Kreutz M, Kulis M, Lopez V, Nair SS, Paul DS, Plongthongkum N, Qu W, Queirós AC, Reinicke F, Sauter G, Schlomm T, Statham A, Stirzaker C, Strogantsev R, Urdinguio RG, Walter K, Weichenhan D, Weisenberger DJ, Beck S, Clark SJ, Esteller M, Ferguson-Smith AC, Fraga MF, Guldberg P, Hansen LL, Laird PW, Martín-Subero JI, Nygren AO, Peist R, Plass C, Shames DS, Siebert R, Sun X, Tost J, Walter J, Zhang K.
Affiliation: The BLUEPRINT consortium
Recommended Application
Identification of DNA methylation patterns for 38 clinically relevant DNA methylation markers (A subset of the targets in Publication) and determination of bisulfite conversion efficiency and workflow success.
Recommended Configuration
Sample per Chip: 16 per 530 chip for Chef ExT templating (15 samples + 1 NTC)
Sample Type
Genomic DNA or FFPE DNA (Bisulfite converted DNA required for library production)
*Duplicate control gDNA samples of average methylation state across all CpGs of approximately >98%, <5%, and an equal mixture of the two equaling ~52% methylation states were run with the panel listed above.
Disease Research Area: Cancer Research
Number of sample in Publication
N/A
Observed Performance*
Panel uniformity: not critical for panel performance (observed >80%)
Reads on-targets: not critical for panel performance (observed >84%)
Average mapped reads: ~250,000
Average mean depth: ~9,400
Input DNA required
Recommended 10 to100ng DNA per sample. For FFPE DNA, 20 to 100ng per sample is recommended.
10 ng used in the control study*
Description of the plugin: The methylation_analysis plugin performs alignment and methylation calling for amplicons on both the Watson (W) and Crick (C) strands. Each amplicon may have zero, one or more designated CpG targets (hotspots) of interest. A summary report shows each barcode name along with the sample name, the total number of reads covering the target CpGs, and the percentage of those reads that are methylated. In addition, for each barcode, text files are generated giving the number of methylated reads, unmethylated reads and percent methylation for each amplicon. There are separate text files for the designated target CpGs, all CpGs in the amplicon insert and all non CpG Cs in the amplicon insert. This plugin has been tested using the Ion AmpliSeq™ Methylation Panel for Cancer Research only. If you choose to use this plugin for any panel other than the Ion AmpliSeq™ Methylation Panel for Cancer Research you must validate it for your purposes. We can’t attest to the quality of the results with a custom panel. This product is labeled For research use only. Not for use in diagnostic procedures.
*Based on the data from the 6 control samples of commercially available human methylated & unmethylated DNA standard set. The DNA standards are purified from HCT116 DKO cells that contain genetic knockouts of DNA methyltransferases, DNMT1 (-/-) and DNMT3b (-/-) , and the unmethylated standard has less than 5% methylated DNA. The human methylated DNA standard has been methylated enzymatically at all CpG dinucleotides by M. SssI methyltransferase.
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Ion AmpliSeq™ Inherited Cancer Research Panel provides a quick, accurate and cost effective way to identify genetic mutations in 134 genes associated with inherited cancers.
Research to identify specific genetic causes of inherited cancers is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Ion AmpliSeq™ Inherited Cancer Research Panel was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Ion AmpliSeq™ Comprehensive Ovarian Cancer Research Panel provides a quick, accurate and cost effective way to identify genetic mutations in 41 genes associated with inherited ovarian cancer.
Research to identify specific genetic causes of inherited ovarian cancer is important but can be difficult because of pleiotropy, locus heterogeneity and accessibility of information. The Ion AmpliSeq™Comprehensive Ovarian Cancer Research Panel was designed based on extensive curation of peer-reviewed literature, disease research databases and consultation with key opinion leaders.
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
This panel amplifies regions covering germline mutations of 25 hereditary cancer-related genes which have a central role in DNA repair and the mismatch repair pathway. This panel is designed to augment a separate BRCA1/2 analysis.
Approximately 5–10% of all breast and/or ovarian cancer cases are considered as inherited. BRCA1 and BRCA2 tumor suppressor genes account for a high penetrance of hereditary cases, but familial cases without mutations in these genes can also occur. Despite their low penetrance, other hereditary cancer-related genes are known to be associated with breast and ovarian cancer risk. This panel amplifies regions covering germline mutations of 25 hereditary cancer-related genes which have a central role in DNA repair and the mismatch repair pathway (APC, ATM, BARD1, BMPR1A, BRIP1, CDH1, CDK4, CDKN2A, CHEK2, EPCAM, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, SMAD4, STK11, and TP53). This panel is designed to augment a separate BRCA1/2 analysis.
Design Date
MARCH 2015
Publication: Hirotsu et al., Multigene panel analysis identified germline mutations of DNA repair genes in breast and ovarian cancer. Molecular Genetics & Genomic Medicine(2015); 3(5): 459–466
Author: Dr. Hirotsu et al.,
Affiliation: Yamanashi Prefectual Central Hospital (Japan)
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
This panel was developed as a research method to identify genetic mutations associated with inherited breast and ovarian cancers. The panel assesses 11 genes known to harbour mutations related to breast and/or ovarian cancer.
Approximately 7-10% of breast and ovarian cancers are hereditary.
BRCA 1 & BRCA 2 tumor suppressor genes account for a high number of these
cases, but it is known that other hereditary cancer related genes are
associated with the risk to develop breast and/or ovarian cancer.The panel
was developed as a research method to identify genetic mutations associated with
inherited breast and ovarian cancers. The panel assesses 11 genes known to
harbour mutations related to breast and/or ovarian cancer (ATM, BRCA1, BRCA2, CHEK2,
PALB2, RAD51C, RAD51D, NBN, CDH1, SMARCA4, TP53). The panel
was validated in 3 laboratories using 45 samples.
Design Date
June 2015
Recommended Application Germ line mutation detection
Recommended
Configuration
Sample Type High molecular weight DNA
PGM
Sample per Chip:
4 per 318 chip
Minimum coverage: 1517x
S5
Sample per Chip:
9 per 540 chip
Minimum coverage: 4600x
Number of sample in
Study
45 samples
Observed
Performance
Input DNA required
10ng per tube
PGM
Panel uniformity: 94.49%
Reads on-targets: 96.29%
S5
Panel uniformity: 89.71%
Reads on-targets: 87%
Disease Research Area: Breast and Ovarian cancer Research
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
Genes in this panel are involved in Cell Cycle & Proliferation, Virology, Signal Transduction.
Ion AmpliSeq™ RNA MAPK Pathway Research Panel targets 197 genes in MAPK pathway that is commonly involved in cell signaling process such as growth, differentiation and proliferation.
Design Date
June 2016
Recommended Application
Gene Expression
Recommended Configuration
Compatible with all Ion Sequencing platform and chips.
We recommend an average of 5000 reads per amplicon for an Ion AmpliSeq™ RNA library (~900,000 total reads) as a starting point for experimental planning. The actual sequencing depth required will depend on the expression levels of the gene targets in your sample RNA.
Sample Type
RNA
Number of Targets
197 genes
# of Primer Pools
1
Input DNA
1-100ng, FFPE compatible
Disease Research Area: Signaling Pathway Research
Ion AmpliSeq™ RNA Human Oncology Pathways Research Panel
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
Genes in this panel are involved in key pathways of cancer.
Ion AmpliSeq™ RNA Human Oncology Pathways Research Panel targets 605 genes related to DNA repair, angiogenesis, cell adhesion, extracellular matrix, cell cycle and apoptosis, and many of the genes encoding kinases and transcription factors that have been found to be differentially expressed between different stages of cancer.
Design Date
June 2016
Recommended Application
Gene Expression
Recommended Configuration
Compatible with all Ion Sequencing platform and chips.
We recommend an average of 5000 reads per amplicon for an Ion AmpliSeq™ RNA library (~3M total reads) as a starting point for experimental planning. The actual sequencing depth required will depend on the expression levels of the gene targets in your sample RNA.
Sample Type
RNA
Number of Targets
605 genes
# of Primer Pools
1
Input DNA
1-100ng, FFPE compatible
Disease Research Area: Oncology Research
Ion AmpliSeq™ RNA WNT Signaling Pathway Research Panel
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
Genes in this panel are involved in regulating WNT pathway, Biomarker-Related Pathway(s), Extracellular Matrix & Cell Adhesion, Oncology, Apoptosis.
Ion AmpliSeq™ RNA WNT Signaling Pathway Research Panel targets 169 genes that regulate the production of WNT signaling molecules, interactions with receptors on target cells, and signal transduction.
Design Date
June 2016
Recommended Application
Gene Expression
Recommended Configuration
Compatible with all Ion Sequencing platform and chips.
We recommend an average of 5000 reads per amplicon for an Ion AmpliSeq™ RNA library (~800,000 total reads) as a starting point for experimental planning. The actual sequencing depth required will depend on the expression levels of the gene targets in your sample RNA.
Sample Type
RNA
Number of Targets
169 genes
# of Primer Pools
1
Input DNA
1-100ng, FFPE compatible
Disease Research Area: Signaling Pathway Research
Ion AmpliSeq™ RNA Pancreatic Adenocarcinoma Research Panel
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
Genes in this panel are involved in Pancreatic carcinoma.
Ion AmpliSeq™ RNA Pancreatic Adenocarcinoma Research Panel targets 92 known genes over-expressed in Pancreatic carcinoma including the RTKs, EGFR and/or its family members (like Her2), and TGF-BetaRs. The activation of RTKs trigger a signaling cascade, which involves SOS, Src, GRB2, and MAPK activation, ultimately resulting in a cellular proliferative response.
Design Date
June 2016
Recommended Application
Gene Expression
Recommended Configuration
Compatible with all Ion Sequencing platform and chips.
We recommend an average of 5000 reads per amplicon for an Ion AmpliSeq™ RNA library (~400,000 total reads) as a starting point for experimental planning. The actual sequencing depth required will depend on the expression levels of the gene targets in your sample RNA.
Sample Type
RNA
Number of Targets
92 genes
# of Primer Pools
1
Input DNA
1-100ng, FFPE compatible
Disease Research Area: Pancreatic Adenocarcinoma Research
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
Genes shown to have a role in breast cancer development and progression.
Ion AmpliSeq™ RNA Breast Cancer Research Panel targets 1174 genes known to be associated with breast cancer development and progression. The gene list was derived from the following eight publications.
Design Date
June 2016
Publications
1. Differential expression of breast cancer-associated genes between stage- and age-matched tumor specimens from African- and Caucasian-American Women diagnosed with breast cancer; J M Grunda, A D Steg, Q He, M R Steciuk, S Byan-Parker, M R Johnson and W E Grizzle; BMC Research Notes 2012, 5:248
2. A Molecular Role for lysyl oxidase in breast cancer invasion; Kirschmann DA, Seftor EA, Fong SF, Nieva DR, Sullivan CM, Edwards EM, Sommer P, Csiszar K, Hendrix MJ; Cancer Res. 2002 Aug 1;62(15):4478-83
3. Down-Regulation of HP1Hs Expression Is Associated with the Metastatic Phenotype in Breast Cancer1; D A. Kirschmann, R A. Lininger, L Gardner, E A Seftor, V A Odero, A M Ainsztein, W C Earnshaw, L L Wallrath, and M J Hendrix; Cancer Research 60, 3359–3363, July 1, 2000
4. Differential Gene Expression in Primary Breast Tumors Associated with Lymph Node Metastasis; Ellsworth RE, Field LA, Love B, Kane JL, Hooke JA, Shriver CD; Int J Breast Cancer, 2011; 2011:142763.
5. Gene That Regulates Breast Cancer Metastasis Identified; Science Daily; http://www.sciencedaily.com/releases/2009/10/091005161322.htm
6. Gene May Cause Some Breast Cancers to Metastasize; BreastCancer.org; http://www.breastcancer.org/research-news/20090105
7. A Six-Gene Signature Predicting Breast Cancer Lung Metastasis; Landemaine T, Jackson A, Bellahcène A, Rucci N, Sin S, Abad BM, Sierra A, Boudinet A, Guinebretière JM, Ricevuto E, Noguès C, Briffod M, Bièche I, Cherel P, Garcia T, Castronovo V, Teti A, Lidereau R, Driouch K; Cancer Res, 2008 Aug 1; 68(15):6092-9
8. Rrp1b, a New Candidate Susceptibility Gene for Breast Cancer Progression and Metastasis; N S Crawford, X Qian, A Ziogas, A G Papageorge, B J Boersma, R C Walker, L Lukes, W L Rowe, J Zhang, S Ambs, D R Lowy, H Anton-Culver, K W Hunter; PLOS Genetics.
Recommended Application
Gene Expression
Recommended Configuration
Compatible with all Ion Sequencing platform and chips.
We recommend an average of 5000 reads per amplicon for an Ion AmpliSeq™ RNA library (~5M total reads) as a starting point for experimental planning. The actual sequencing depth required will depend on the expression levels of the gene targets in your sample RNA.
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
Genes in this panel involves long non coding RNAs that are known tumor suppressors.
Ion AmpliSeq™ Long Non-coding RNA (lncRNA) Research Panel targets 418 lncRNAs involved in key biological processes. Specific targets included in the panel are known tumor suppressors GAS5, NEAT1, CAHM, MIR31HG and MIR7-3HG as well as known oncogenes HOTAIR, MALAT1, H19, XIST, HULC, TUG1, SNHG16, and LINC00152.
Design Date
June 2016
Recommended Application
Gene Expression
Recommended Configuration
Compatible with all Ion Sequencing platform and chips.
We recommend an average of 5000 reads per amplicon for an Ion AmpliSeq™ RNA library (~2M total reads) as a starting point for experimental planning. The actual sequencing depth required will depend on the expression levels of the gene targets in your sample RNA.
Sample Type
RNA
Number of Targets
418 genes
# of Primer Pools
1
Input RNA
1-100ng, FFPE compatible
Disease Research Area: Long Non-coding RNA Research
This file contains all of the data for your 384 Well Plate. For each amplicon, you will find the pool information, its (row,column) coordinates, the AmpliconID, and the forward and reverse primers.
BRCA1_2.YYYYMMDD.concentration.tab
This file contains the concentration.
BRCA1_2.YYYYMMDD.designed.bed
Details the regions covered by the panel. This file is used for data analysis with the Torrent Browser / Variant Caller Plug-In.
BRCA1_2.YYYYMMDD.hotspotAnnot.csv
This file provides a list of the genes associated with each Fixed Panel, listed in cosmic id order and contains the following information:
* Gene symbol
* Accession id
* COSMIC id
* CDS Mutation - change occurred in the nucleotide sequence
* AA Mutation - change occurred in the peptide sequence as a result of the mutation
* Strand (+/-)
* Coordinates (hg19)
* Amplicon ID
* Insert Sequence
* Target URL – links to the COSMIC curated mutations database.
BRCA1_2.YYYYMMDD.hotspots.bed
The Hotspots BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels*.
* Note: To avoid the issue of ambiguous right alignment of indel calling, the Hotspots BED files are left aligned for optimal performance when used with Torrent Suite Variant Caller.
BRCA1_2.YYYYMMDD.primerDataSheet.csv
This file presents detailed information for the amplicons in the panel: a (sorted) amplicon ID number, the forward and reverse primers, the gene symbol, chromosome number and the (start,end) coordinates for the amplicon and for the insert (the amplicon without considering the primer length).
BRCA1_2.YYYYMMDD.results_coverage_details.csv
This file contains the coverage details for the panel. This results file contains information about the Gene symbol, the Chromosome number and the start, end coordinates of each region covered, the number of amplicons required to cover that region, the number of bases that were covered, the number of targeted bases, the number of missed bases and the proportion of coverage.
BRCA1_2.YYYYMMDD.results_coverage_summary.csv
In this file you will find for each gene, the chromosome number, the total number of amplicons, total number of bases submitted to design, the number of bases that were covered and the overall coverage (Covered bases/Total Bases). The number of exons in each entry point is available, as well as a distribution of the number of exons that were covered in proportion of 1, > 0.95, > 0.9, > 0.8, > 0.7, > 0.5, > 0.2, < 0.2 and at 0.
BRCA1_2.YYYYMMDD.submitted.bed
This file contains the regions that were submitted to AmpliSeq for design.
JSON formatted file with optimized parameters to be manually uploaded for variant calling on TVC 4.0 for PGM runs
plan.json
This file contains all the information to automatically configure a run plan for this panel, when the panel's files are directly downloaded from the Torrent Server as shown below.
Data Analysis in the Torrent Browser
You can easily create a plan run on the Torrent Browser to analyze AmpliSeq panels by directly downloading them from your account at ampliseq.com.
1) Find and click the "AmpliSeq.com Import" link on the AmpliSeq section of the Plan tab.
2) You will be asked to input your AmpliSeq.com login information:
3) Select the appropriated panel; in this case we will select the BRCA1 and BRCA2 Panel
4) After clicking the "Import Selected" button a download screen displays the status of the download. Reload the page to verify the download is complete.
5) Once the download has finished, verify that the plan is available in the Ampliseq DNA Plans table: the plan is ready to be used.
Summary:
Mutations in tumor suppressor genes BRCA1 and BRCA2 have been implicated in hereditary breast and ovarian cancer. The Ion AmpliSeq™ BRCA1/2 Panel utilizes 167 amplicons to analyze the coding regions of both BRCA1 and BRCA2 genes.
Description
Mutations in tumor suppressor genes BRCA1 and BRCA2 have been implicated in hereditary breast and ovarian cancer. Much research is currently being done today to better detect, treat, and prevent cancer by assessing mutations in those who carry mutations in BRCA1 and BRCA2. The Ion AmpliSeq™ BRCA1/2 Panel utilizes 167 amplicons to analyze the coding regions of both BRCA1 and BRCA2. Design and validation is currently in progress with Drs. Marjolijn Ligtenberg and Arjen Mensenkamp from Radboud University Nijmegen Medical Centre, The Netherlands, and with Drs. José Carlos Machado and José Luis Costa from The Institute of Molecular Pathology and Immunology of the University of Porto.
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Ion AmpliSeq™ Cancer Hotspot Panel v2 is a single pool of primers used to perform multiplex PCR for preparation of amplicon libraries from genomic "hot spot" regions that are frequently mutated in human cancer genes. This panel contains 207 amplicons in 1 pool.
The Ion AmpliSeq™ Cancer Hotspot Panel v2 is a single pool of primers used to perform multiplex PCR for preparation of amplicon libraries from genomic "hot spot" regions that are frequently mutated in human cancer genes. Building on the mutations included in our original Ion AmpliSeq™ Cancer Panel, this latest Ion AmpliSeq™ ready-to-use panel provides:
Maintained compatibility with FFPE samples while expanding mutational content for broader coverage of additional genes and "hot spot" mutations
Extremely uniform coverage for more efficient sequencing and cost savings
Enhanced primer design with optimization of new primer sets and even lower strand bias for added confidence in accurate variant calling
Improved variant detection with Torrent Suite™ Software v3.0 and Variant Caller Plugin in low allele variant detection along with improved indel sensitivity
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Ion AmpliSeq™ Colon and Lung Cancer Panel v2 is a single pool panel that analyses hotspot and targeted regions of 22 genes implicated in colon and lung cancers. This panel uses 92 amplicons for re-sequencing and analysis. (**Note: The trial kit version is not available for EMEA countries**)
Designed with leading researchers from the OncoNetwork Consortium, the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 is a single pool panel that analyse hotspot and targeted regions of 22 genes implicated in colon and lung cancers (KRAS, EGFR, BRAF, PIK3CA, AKT1, ERBB2, PTEN, NRAS, STK11, MAP2K1, ALK, DDR2, CTNNB1, MET, TP53, SMAD4, FBXW7, FGFR3, NOTCH1, ERBB4, FGFR1, FGFR2). It contains the same primer pairs of the Ion AmpliSeq™ Colon and Lung Cancer Panel v1 plus three new amplicons covering additional target regions for NRAS and ALK gene. NRAS exon 4 variants ( p.117, p.146) and ALK (G1269A, p.S1206Y)
Design Date
January 2014
Recommended Configuration
Sample per Chip: 8 per 316 chip
Minimum coverage: 500x
Each row contains details about the regions covered by the panel: the chromosome number, the start and ending positions, the gene ID associated to the region and the pool ID in which the primers are placed. This file is used for data analysis with the Torrent Browser / Variant Caller Plug-In; the primer pool information is used by the Coverage Analysis plugin to display a plot of the average number of reads per amplicon per pool:
CCP.YYYYMMDD.hotspots.bed
The Hotspots BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels*.
* Note: To avoid the issue of ambiguous right alignment of indel calling, the Hotspots BED files are left aligned for optimal performance when used with Torrent Suite Variant Caller.
CCP.YYYYMMDD.missed.bed
This file contains information about the regions that are missed by the design: the chromosome number and the (start,end) coordinates of the missed region.
CCP.YYYYMMDD.primerDataSheet.csv
This file presents detailed information for the amplicons in the panel: a (sorted) amplicon ID number, the forward and reverse primers, the gene symbol, chromosome number and the (start,end) coordinates for the amplicon and for the insert (the amplicon without considering the primer length).
CCP.YYYYMMDD.results_coverage_details.csv
This file contains the coverage details for the panel. This results file contains information about the Gene symbol, the Chromosome number and the start, end coordinates of each region covered, the number of amplicons required to cover that region, the number of bases that were covered, the number of targeted bases, the number of missed bases and the proportion of coverage.
CCP.YYYYMMDD.results_coverage_summary.csv
In this file you will find for each gene, the chromosome number, the total number of amplicons, total number of bases submitted to design, the number of bases that were covered and the overall coverage (Covered bases/Total Bases). The number of exons in each entry point is available, as well as a distribution of the number of exons that were covered in proportion of 1, > 0.95, > 0.9, > 0.8, > 0.7, > 0.5, > 0.2, < 0.2 and at 0.
CCP.YYYYMMDD.submitted.bed
This file contains the regions that were submitted to AmpliSeq for design.
JSON formatted file with optimized parameters to be manually uploaded for variant calling on TVC 4.0 for Proton runs
plan.json
This file contains all the information to automatically configure a run plan for this panel, when the panel's files are directly downloaded from the Torrent Server as shown below.
Data Analysis in the Torrent Browser
You can easily create a plan run on the Torrent Browser to analyze AmpliSeq panels by directly downloading them from your account at ampliseq.com. The following example for the BRCA panel applies as well for the CCP panel.
1) Find and click the "AmpliSeq.com Import" link on the AmpliSeq section of the Plan tab.
2) You will be asked to input your AmpliSeq.com login information:
3) Select the appropriated panel; in this case we will select the BRCA1 and BRCA2 Panel
4) After clicking the "Import Selected" button a download screen displays the status of the download. Reload the page to verify the download is complete.
5) Once the download has finished, verify that the plan is available in the Ampliseq DNA Plans table: the plan is ready to be used.
Summary:
The Ion AmpliSeq™ Comprehensive Cancer Panel provides highly multiplexed target selection of genes implicated in cancer research. With all-exon coverage of 409 genes, this panel delivers fast, FFPE-compatible, target selection for a broad survey of key genes for semiconductor sequencing. The panel contains 15,992 amplicons in only 4 pools.
The Ion AmpliSeq™ Comprehensive Cancer Panel provides highly multiplexed target selection of genes implicated in cancer research. Encompassing over 50% of the Wellcome Trust Sanger Institute Cancer Gene Census, this is the most comprehensive cancer gene panel available. With all-exon coverage of 409 genes, the Ion AmpliSeq™ Comprehensive Cancer Panel delivers fast, FFPE-compatible, target selection for a broad survey of key genes for semiconductor sequencing.
The Ion AmpliSeq™ technology allows ultra-high multiplex PCR combined with targeted sequencing library construction in just 16 hours for over 400 genes. Utilizing only 10 ng of input DNA per primer pool for a total of 40 ng of input DNA, analysis of restricted samples like FFPE samples is possible. The Ion AmpliSeq™ Comprehensive Cancer Panel is optimized for library construction with the Ion AmpliSeq™ Library Kit 2.0. Libraries are then ready for template preparation on the Ion OneTouch™ System and sequencing on the Ion PGM™ Sequencer. The Ion AmpliSeq™ Comprehensive Cancer Panel is not compatible with Ion Ampliseq™ 2.0 Beta Kits.
Learn more
COSMIC mutation targets
15,749
Amplicon length
125–175 bp (average 155 bp)
Primer pool size
~16,000 primers in 4 tubes
Input DNA required
10 ng per pool, 40 ng per DNA sample
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The TP53 gene codes the tumor suppressor protein p53 which has been extensible researched in the field of Human Oncology. The Ion AmpliSeq™ TP53 Panel is a 2 pool panel with 24 amplicons designed to analyze all coding exons of the TP53 gene.
Description
The tumor suppressor protein p53 is encoded by the TP53 gene, one of the most researched genes in human cancer. Genetic mutations in TP53 can impact gene expression of p53 and its downstream targets, and TP53 mutations are present in more than 50% of all types of human cancers. With input from Anne-Lise Børresen-Dale and her lab at the Norwegian Radium Hospital, Institute for Cancer Research, the Ion AmpliSeq™ TP53 Panel was designed and verified to analyze all coding exons of TP53 with 24 amplicons, enabling the advancement of cancer research in early detection, prevention, and therapy.
**Note that for the Ion AmpliSeq TP53 Panel, your order will contain only 750 pre-pooled reactions in tubes, no primer plates will be included in your order.
This file contains all of the data for your 384 Well Plate. For each amplicon, you will find the pool information, its (row,column) coordinates, the AmpliconID, and the forward and reverse primers.
ColonLung.YYYYMMDD.concentration.tab
This file contains the concentration (not sure if this is customer facing)
ColonLung.YYYYMMDD.designed.bed
Details the regions covered by the panel. This file is used for data analysis with the Torrent Browser / Variant Caller Plug-In.
ColonLung.YYYYMMDD.hotspotAnnot.csv
This file provides a list of the genes associated with each Fixed Panel, listed in cosmic id order and contains the following information:
Gene symbol
Accession id
COSMIC id
CDS Mutation - change occurred in the nucleotide sequence
AA Mutation - change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon ID
Insert Sequence
Target URL – links to the COSMIC curated mutations database.
ColonLung.YYYYMMDD.hotspots.bed
The Hotspots BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels*.
* Note: To avoid the issue of ambiguous right alignment of indel calling, the Hotspots BED files are left aligned for optimal performance when used with Torrent Suite Variant Caller.
ColonLung.YYYYMMDD.primerDataSheet.csv
This file presents detailed information for the amplicons in the panel: a (sorted) amplicon ID number, the forward and reverse primers, the gene symbol, chromosome number and the (start,end) coordinates for the amplicon and for the insert (the amplicon without considering the primer length).
ColonLung.YYYYMMDD.results_coverage_summary.csv
In this file you will find for each gene, the chromosome number, the total number of amplicons, total number of bases submitted to design, the number of bases that were covered and the overall coverage (Covered bases/Total Bases). The number of exons in each entry point is available, as well as a distribution of the number of exons that were covered in proportion of 1, > 0.95, > 0.9, > 0.8, > 0.7, > 0.5, > 0.2, < 0.2 and at 0.
ColonLung.YYYYMMDD.submitted.bed
This file contains the regions that were submitted to AmpliSeq for design.
JSON formatted file with optimized parameters to be manually uploaded for variant calling on TVC 4.0 for PGM runs
plan.json
This file contains all the information to automatically configure a run plan for this panel, when the panel's files are directly downloaded from the Torrent Server as shown below.
Data Analysis in the Torrent Browser
You can easily create a plan run on the Torrent Browser to analyze AmpliSeq panels by directly downloading them from your account at ampliseq.com. The following example for the BRCA panel applies as well for the Colon and Lung panel.
1) Find and click the "AmpliSeq.com Import" link on the AmpliSeq section of the Plan tab.
2) You will be asked to input your AmpliSeq.com login information:
3) Select the appropriated panel; in this case we will select the BRCA1 and BRCA2 Panel
4) After clicking the "Import Selected" button a download screen displays the status of the download. Reload the page to verify the download is complete.
5) Once the download has finished, verify that the plan is available in the Ampliseq DNA Plans table: the plan is ready to be used.
Summary:
The Ion AmpliSeq™ Colon and Lung Cancer Panel is a single pool panel that analyses hotspot and targeted regions of 22 genes implicated in colon and lung cancers. This panel uses 90 amplicons for re-sequencing and analysis.
Designed with leading researchers from the OncoNetwork Consortium, the Ion AmpliSeq™ Colon and Lung Cancer Panelv1 is a single pool that contains 90 primer pairs to analyze hotspot and targeted regions of 22 genes implicated in colon and lung cancers (KRAS, EGFR, BRAF, PIK3CA, AKT1, ERBB2, PTEN, NRAS, STK11, MAP2K1, ALK, DDR2, CTNNB1, MET, TP53, SMAD4, FBXW7, FGFR3, NOTCH1, ERBB4, FGFR1, FGFR2).
Design Date
February 2013
Recommended Configuration
Sample per Chip: 8 per 316 chip
Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel Files
CSV file
The CSV file in this panel contains the assay names and references of the 61 unique gene fusions, 5
expression control genes, and 4 genes containing 5’ and 3’ imbalance assays. As indicated in the reference column, some EML4-ALK assays target fusions transcripts having updates to annotation in COSMIC v67 (denoted as COSFXXXX.1)
README
The README text file provides information
about the panel design and analysis software solution.
Summary:
Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel is designed to target a set of known fusion transcripts as well as expression imbalances between the 3’ and 5’ regions of the genes. The panel contains 85 amplicons in a single pool. (**Note: The trial kit version is not available for EMEA countries**)
This panel targets over 70 known fusion transcripts for the ALK, RET, ROS1, and NTRK genes. In addition, the panel contains amplicons to analyze the expression imbalance between the 3’ and 5’ regions of these genes, which allows the discovery of novel mutations associated with the ALK gene. It also includes 5 positive controls, which help determine RNA quality and overall assay performance.
Design Date
July 2014
Recommended Configuration
Sample per Chip: 16 per 318 chip
Sample Type
FFPE samples
Recommended Application
Gene Fusion Detection
Observed Performance
Sensitivity to detect targeted fusion transcript when present in only 1% of input RNA. Over 90% concordant with cytogenetic methods for ALK fusion detection.
This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):
Gene symbol
Accession id
COSMIC id
CDS Mutation - Change occurred in the nucleotide sequence
AA Mutation - Change occurred in the peptide sequence as a result of the mutation
Strand (+/-)
Coordinates (hg19)
Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
Insert Sequence
Target URL – Links to the COSMIC curated mutations database.
Designed BED file
The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)
HotSpot BED file
The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.*
Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).
* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.
Data Analysis in Torrent Browser
To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files. In the case of the "Ion AmpliSeq™ Pan-Bacterial Research Panel" and the "Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research Panel", the panel files cannot be directly imported into the the Torrent Browser using the upload function or by direct import of the files. Please use the appropriate plugin for analysis purposes.
For Torrent Suite Software 4.x and 5.x
Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.
For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.
The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.
For Torrent Suite Software 3.x
Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.
Next
Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:
Select your Target Regions and Hotspot Regions BED files from the drop-down menus:
* The designer currently only works for Human Reference Genome, hg19.
Summary:
The Ion AmpliSeq™ AML Cancer Research Panel is a 4 pool panel utilizing 237 amplicons to analyze 19 genes implicated in acute myeloid leukemia.
As the incidence of acute myeloid leukemia (AML) increases, additional research becomes increasingly important to better understand the genes and mutations involved. The Ion AmpliSeq™ AML Cancer Research Panel utilizes 237 amplicons to analyze 19 genes implicated in AML (entire coding regions: CEBPA, DNMT3A, GATA2, TET2, TP53; hotspot regions: ASXL1, BRAF, CBL, FLT3, IDH1, IDH2, JAK2, KIT, KRAS, NPM1, NRAS, PTPN11, RUNX1, WT1).
*Additional testing is currently in progress with Rosemary Gale, UCL Cancer Institute, London, United
Kingdom; Claude Preud’homme, Centre Hospitalier Régional Universitaire (CHRU)
de Lille, France; Jacqueline Schoumans, Centre Hospitalier Universitaire
Vaudois (CHUV), Lausanne, Switzerland and Christian Thiede, Technical
University Dresden, Germany
Design Date
June 2014
Recommended Configuration
6 Sample per Ion 318™ Chip
amplicons with target base coverage at 500X: >95%
The ready-to-use design details are available for download. In a compressed folder, there are a number of files with diverse information. Although the type of data in all of the files is plain text and they can be opened using any text editor, we recommend using a spreadsheet such as MS Excel for viewing their contents given their multicolumn format.
Apoptosis_Designed.bed
This file contains the RefSeq accession number of the RNA sequence (transcript) for which the primers were designed, the start and end coordinates of the amplicon relative to the transcript sequence, the amplicon ID and in the last column the HGNC gene symbol that is associated with the transcript identifier in the first column. The file contains one row for each gene or accession number submitted to design.
Note: the contents in this file are not viewable in the UCSC genome browser given that the RefSeq coordinates that it reports are not compatible with the browser.
Apoptosis_Primer.bed
This file provides similar but more detailed information than the file Apoptosis_Designed.bed . There are differences in the format of some columns and in the number of rows; the differences in format make this file compatible with the UCSC genome browser. This file presents two rows for each one of all of the targets submitted to design: one row for the forward primer and one row for the reverse primer. The start and end coordinates are for the position of the primer on the chromosome that is displayed in column 1. The second to last column reports the preferred TaqMan assay that can be used for verification. Also the gene symbol in the last column corresponds to the symbol submitted by the user (it might or might not be the HGNC symbol).
Apoptosis_DataSheet.csv
This file contains one row for each of the RefSeq accession numbers of the RNA sequences that are covered by the designed primers. For each row there is extensive information such as the names submitted by the user, the corresponding HGNC approved symbol, the amplicon ID, the sequence of the forward and reverse primers, the start and end coordinates of the primers relative to the RefSeq sequence, the coordinates of the start and end of the amplicon and the start and end of the insert sequence relative to their position in the chromosome and the strand of the chromosome in which the sequence is located.
Summary:
The Ion AmpliSeq™ RNA Apoptosis Panel is a screening tool designed against 267 genes involved in the cellular apoptosis pathway. Included are genes associated with death receptor mediated apoptosis, cmyc, and p53 mediated apoptosis. This panel contains 267 amplicons in 1 pool.
The Ion AmpliSeq™ RNA Apoptosis Panel is a screening tool designed against 267 genes involved in the cellular apoptosis pathway. Included are genes associated with death receptor mediated apoptosis, cmyc, and p53 mediated apoptosis.
Measure gene expression fold changes between samples
Amplicons are designed to be most inclusive for transcripts of the target gene
Each reaction requires only 500 pg of unfixed RNA or 5 ng of fixed (FFPE) RNA
Prepare amplicon libraries with the Ion AmpliSeq™ RNA Library Kit and sequence on the Ion Personal Genome Machine™ (PGM™) or Proton™ System
This panel contains 267 amplicons (534 primers), approximately 150 bases in length, in a single pool. Learn more
For Research Use Only. Not intended for human or animal therapeutic or diagnostic use.
Targets
267
Amplicon length
Average 150 bp
Primer pool size
534 individual primers, 267 primer pairs
The ready-to-use design details are available for download. In a compressed folder, there are a number of files with diverse information. Although the type of data in all of the files is plain text and they can be opened using any text editor, we recommend using a spreadsheet such as MS Excel for viewing their contents given their multicolumn format.
Cancer50_Designed.bed
This file contains the RefSeq accession number of the RNA sequence (transcript) for which the primers were designed, the start and end coordinates of the amplicon relative to the transcript sequence, the amplicon ID and in the last column the HGNC gene symbol that is associated with the transcript identifier in the first column. The file contains one row for each gene or accession number submitted to design.
Note: the contents in this file are not viewable in the UCSC genome browser given that the RefSeq coordinates that it reports are not compatible with the browser.
Cancer50_Primer.bed
This file provides similar but more detailed information than the file Cancer50_Designed.bed . There are differences in the format of some columns and in the number of rows; the differences in format make this file compatible with the UCSC genome browser. This file presents two rows for each one of all of the targets submitted to design: one row for the forward primer and one row for the reverse primer. The start and end coordinates are for the position of the primer on the chromosome that is displayed in column 1. The second to last column reports the preferred TaqMan assay that can be used for verification. Also the gene symbol in the last column corresponds to the symbol submitted by the user (it might or might not be the HGNC symbol).
Cancer50_DataSheet.csv
This file contains one row for each of the RefSeq accession numbers of the RNA sequences that are covered by the designed primers. For each row there is extensive information such as the names submitted by the user, the corresponding HGNC approved symbol, the amplicon ID, the sequence of the forward and reverse primers, the start and end coordinates of the primers relative to the RefSeq sequence, the coordinates of the start and end of the amplicon and the start and end of the insert sequence relative to their position in the chromosome and the strand of the chromosome in which the sequence is located.
Summary:
The Ion AmpliSeq™ RNA Cancer Panel is a screening tool designed against 50 oncogenes/tumor suppressor genes found in the COSMIC database. This panel has been developed as an RNA complement to the DNA focused Ion AmpliSeq™ Cancer Hotspot Panel v2. This panel contains 50 amplicons in 1 pool.
The Ion AmpliSeq™ RNA Cancer Panel is a screening tool designed against 50 oncogenes/tumor suppressor genes found in the COSMIC database. This panel has been developed as an RNA complement to the DNA focused Ion AmpliSeq™ Cancer Hotspot Panel v2. The panel is a single pool of primers representing 50 oncogenes and tumor suppressor genes with coverage of KRAS, BRAF, and EGFR genes.
Measure gene expression fold changes between samples
Amplicons are designed to be most inclusive for transcripts of the target gene
Each reaction requires only 500 pg of unfixed RNA or 5 ng of fixed (FFPE) RNA
Prepare amplicon libraries with the Ion AmpliSeq™ RNA Library Kit and sequence on the Ion Personal Genome Machine™ (PGM™) or Proton™ System
This panel contains 50 amplicons (100 primers), approximately 150 bases in length, in a single pool.
For Research Use Only. Not intended for human or animal therapeutic or diagnostic use.
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Targets
50
Amplicon length
Average 150 bp
Primer pool size
100 individual primers, 50 primer pairs
2) You will be asked to input your AmpliSeq.com login information:
3) Select the appropriated panel; in this case we will select the BRCA1 and BRCA2 Panel
4) After clicking the "Import Selected" button a download screen displays the status of the download. Reload the page to verify the download is complete.
5) Once the download has finished, verify that the plan is available in the Ampliseq DNA Plans table: the plan is ready to be used.
